Free Me, Free My Soul
by SweetStrawberryShortCake
Summary: A Stargate: Atlantis BDSM universe story. Inspired by both Xanthe and Keira Marcos. Both can be found through google. Completely authorized by Xanthe and Keira Marcos. It might lean on the side more of keiras as I am using her idea of an abused Rodney, but it also might lean more Xanthes way as it might not have pleasure houses of any type. DominantJohn/SubmissiveRodney. MarineJohn
1. Prologue: One Minute

**AN: so here's an idea for a new story. It's a Stargate: Atlantis BDSM universe story. Inspired by both Xanthe and Keira Marcos. Both can be found through google. Completely authorized by Xanthe and Keira Marcos. It might lean on the side more of keiras as I am using her idea of an abused Rodney, but it also might lean more Xanthes way as I might not have pleasure houses of any type of pleasure training. But I don't know right now. Anyways… this is just a simple little chapter. Tell me if you want me to continue it or not. Will be rated M…even slightly MA. Sorry admins. Dominant!John/Submissive! Rodney. Marine!John.**

Free Me, Free My Soul: Prologue: One Minuet

_Stay here, see me come undone. Just free my soul and turn me on._

John Sheppard stood against the wall and just couldn't believe his ears. McKay was just asking for a nice hard strapping. And John could tell by the look on Elizabeth's face that she felt the same. "Rodney, just stop." She bit out as she put her face in her hands.

"I can't just ignore your actions. Colonel Sumner gave you a direct order and you ignored it."

McKay rolled his eyes. "I wasn't done taking readings of the seismic activity on the planet. If we have any hope of helping the people on that planet, I had to get those readings."

She slammed her hand down onto her desk. "Damn it Rodney! You know we could have gone back after the activity stopped. Yet you stayed and risked yourself and Colonel Sumner's team. I can't excuse such behavior. You could have been killed! Do you not realize how mission essential you are!?"

When McKay opened his mouth to respond, she raised her hand and cut him off. "No. fifteen with the strap Rodney. No clothes. In the Discipline Room. WITH AN AUDIENCE." He glared at her. He turned and walked out before either she or John could say anything.

John groaned and followed him out. "McKay!" When the man continued to ignore him, John almost growled in anger. "Submissive!" He watched as McKay stilled, his back straight. John nodded in approval. He walked over and in front of McKay.

"Why in fuck's name are you acting out so much? You know how important you are to this mission yet you act out, you disobey orders, and you constantly put yourself in harm's way." McKay looked up and into John's eyes defiantly.

"Why I do anything I do is none of your business. It's no one's business." McKay whispered, his chin jutting out.

John balled his fists by his side. "Christ! Do you really care so little about yourself? That you would just throw your life away by letting yourself get fatally wounded?" John groaned out.

That made something in McKay snap. "Why should I care about myself? Why should anyone care about me? As long as I do my job, nothing else matters!"

"You really believe that!? Well, maybe you need someone to care about you, to make you care about yourself!"

McKay bodily pushed him that time, his hands landing hard on John's chest and making the Marine wobble slightly.

"DON'T! Don't you dare say what I think you are going to say! The last Domme I trusted betrayed me in every way! Don't you do dare say I need some Dominant to live for! I would much rather live my life alone, taking every punishment those ranked higher than me felt to give me than be with another Dominant. I WILL NEVER TRUST ANOTHER ONE WITH ME!"

Jon caught the hands that were beating down onto his chest. He spun McKay around so they were pressed together chest to back. He sunk them to ground slowly. He had his chin resting gently on McKay's head. He could feel the body beneath him shaking with sobs, rather than hear the sobs themselves.

John was confused. The doctor's file said nothing about an abusive top, yet he was showing every sign. "Shhh. It's okay. You're ok Rodney. You're safe."

John flicked his eyes around them, thanking God it was the middle of the night and there were very few people around them. And thank God they were all people who understood the meaning of discretion. He easily stood and picked McKay up. He had one arm placed around his shoulders and another placed under McKay's knees. He saw one of his Marines, Stackhouse, quickly walk to the transporter and open it. He nodded his head in approval as he entered it with McKay in his arms.

While in the transporter, he looked down at McKay and decided he would get to the bottom of the doctors behavior. He frowned and clumsily pressed the button that would transport him to the tower his room was in.

_Lay me down and stop the time. So long now leave the world behind._

**AN: Typos fixed. haha i apologize for them. im not perfect and i dont trust the reliability of betas. Domme is the shortened version for Female Dominant. Dom is the shortened version of Male Dominant. i also mentioned "Top" can be another way to say Dom or Domme. but can also just mean some one who prefers to give anal sex and not receive. in this story "Top" and "Bottom" will mean Dominant and Submissive. anything else will be explained in the story. **


	2. Chapter 1: Falling Slowly

_**AN: here's the new chapter for Free Me, Free My Soul. I got a review to make the chapters longer, and I will of course do this. But it might take a bit to get the story going. I actually haven't thought this one out. So this story seems to be a bit different than my others as I am just going to see where the story takes me as well as all of you guys. The story starts near the start of the expedition. On a side note…yes I do write from experience. I spent three months in intense 24/7 training. So a lot of my kinks will probably be included in this story and I might fashion Rodney from myself as I too am a submissive. **_

**Free Me, Free My Soul: Chapter One: Falling Slowly **

_I don't know you but I want you all the more for that._

Rodney felt himself drifting on comforting haze of sleep. He could feel the comfortable bed under him, the soft pillow under his head, and the cozy warmth of the blanket over him. He was warm and cozy, and he felt…safe. It was a curious sensation, and it was what brought Rodney out of his sleepy haze. He hadn't felt this safe in quite a while. It was then that he realized that he wasn't exactly in his own bed. He sat up quickly wondering just where the hell he was.

"Hey careful. You had quite the break down earlier. You want to tell me what that was all about Rodney?"

Rodney shifted nervously. "I was collared once before I came to the SGC. By a woman name Eugena. She was very…controlling. And not necessarily in a good way."

The vague explanation had John's hackles rising. "And?" He asked as he settled in the chair in front of his desk.

"And… I was stupid. I thought I was in love with her, so I let get away with a lot. It got...bad and it took a friend from work to get me out of the situation. We had a contract, but she didn't grant me a Safe Word or any type of safety net. I didn't think I needed one because we were once very open with each other. But after a while I started to notice that she had less and less regard for my feelings as well as my safety. But Tyler got me out and kept me safe. And now here I am."

John felt his jaw stiffen. "What- you said in the hallway that she betrayed you in every way. What did she do to you that finally made you leave? How did she hurt you?"

Rodney's eyes darkened. "She just betrayed me Sheppard. I don't want to talk about this anymore." John could tell the conversation was getting to Rodney.

"Um…is there any way you could get Elizabeth to allow me to keep my clothes on? I'm not too crazy about people seeing me naked anymore?"

John had the sickening feeling that the reasons for Rodney not wanting for people to see his body had everything to do with this Domme. John found himself desperately wanting to slap her, with steadily increasing anger.

"I'll talk to her Rodney but I don't know. I'll ask okay." He told the other man gently.

Rodney shifted again and nodded his head. It didn't take long for John to realize it was a nervous habit. John could imagine that if he were McKay's Dom that he would watch very closely for this particular habit.

"Do you want me to walk you back to your quarters?" Rodney shook his head at this.

"No need Colonel, I've got it. But thank you. For everything you did tonight. Will you be in the Discipline Room tomorrow?" Rodney responded as he slid out of the bed and looked around sheepishly for his boots.

John picked them up from beside the door and handed them to Rodney who blushed and sat down on the bed again to slide them on and lace them up.

"I don't know… did you want me there or something?" The blue eyed man looked up at him with hooded lids and said, "Only if you don't mind. It'll make it all…easier. And I'd rather have someone there who…knows."

John gulped. Definitely about the bitch then, or something because of her. He wasn't a dumb man by any means. And he knew what McKay was really saying was "I want you there to run interference and to get me the fuck out of the room before people find themselves asking questions I can't answer."

He nodded. "Of course. I'll be sure to speak with the Mayor on your behalf." They both lingered by the door awkwardly as they said goodnight in a tense roundabout way. Then the Submissive was gone, and John found himself wanting to watch him walk down the hall. But he was also disturbed by what he'd learned. He was resolved to speak with Elizabeth tomorrow.

_Words fall through me and always fool me and I can't react._

_And games that never amount to more than they're meant_

"You don't get it Elizabeth. That Domme, she hurt him, deformed him or scarred him in some way. I just know she did. It would be cruel to put him through that."

"I understand that she damaged him, at least emotionally. You don't have any proof that he is physically damaged. And I can't let what he did go unpunished. For him the humiliation of being naked will be just as much as punishment and the strap will. But, if you are truly worried- and I can tell that you are- you can either do his medical checks, or you can administer the punishment yourself. He IS on your team after all. John rolled this thought around in his head.

"I will do either one, but only if he agrees to it. I won't take that choice away from him." She nodded her head.

"We have an understanding then."

_Will play themselves out_

_Falling slowly, eyes that know me and I can't go back._

John stood outside the room waiting for McKay. It was important that the man know that John was on his side.

"Colonel. Why aren't you inside?" John bowed his head in respect.

"I talked to Elizabeth for you. She didn't concede on the clothes front…but with your permission I can either do your medical checks or I can administer the punishment." He honestly didn't think that McKay was going to go for either of the choices so he was surprised when the man didn't only agree, but asked for John to be the only person handling him.

"I would prefer it actually if you did both. I know you can. You're…well trained after all." The other man said this with the grace to blush a soft pink.

John found his head spinning slightly. McKay had checked up on him…had read his uncensored file. When had this happened? Last night? Before last night? Before they came to Atlantis? Before they left Antarctica? Before they had even met?

Rodney seemed to gaze back at him with a trust that was completely unwarranted and undeserved. He had only ever bickered with the other man, had only ever borderline fought with him. And he was choosing to trust John based purely on the fact that he was well trained. It was an honor to feel so trusted.

And something that had only been peeking at the surface surged forward and out into the open. John had always made sure to keep his dominant self well hidden. He only allowed for the barest minimum of that part of himself to show, as society expected to see it. But with Rodney gazing at him in such a way the Dominant in him couldn't help but feel empowered and strong with such trust being given to him. He bowed his head again and led the man into the hall.

Together they walked to the Kings Cross in the center of room. Elizabeth stepped forward to help Rodney undress and take his clothes. John held his hand up, taking the trust that McKay had put into him seriously. He helped Rodney undress and set his clothes on the table that had all the supplies on it.

_You have suffered enough and warred with yourself, it's time that you won._

John ignored the gasps that filled the empty silence and stood back and took a medical inventory of McKay's body as all of his training dictated. Multiple scars, from deep cutting. A little too deep to be dynamically healthy.

He looked at the way that McKay held his hands and wrists. He reached out and picked his hands up. He felt each wrist, hand, and finger. Both wrists had once been badly broken, and only slightly properly set. His right hand had three once badly broken fingers, also poorly set, and his left hand had two once badly broken fingers.

These were common injuries that correlated with Subs thrashing in their cuffs. He ran his hands down McKay's torso and counted the injured and badly healed ribs. Three ribs on the right, four on the left. He bit the inside of his cheek and touched his hips. Both once cracked, both the rib and hip injuries are constant with injuries sustained when thrashing against a waist restraint.

He audibly sighed in relief when he saw a healthy penis and two testicles. _But if he didn't get these injuries while being castrated then when?_ He slid his hands down, both femurs were healthy, but both knee caps were swollen, indicative with straining against leg restraints. Both of his ankles had been broken and poorly set. He had once had two broken toes on his right foot, and one on his left. He stood up and massaged his shoulders, one shoulder injury. He looked at McKay's lowered face and felt his heart break. He could hear crying in the room but put out of his mind. He spun him around and gazed at Rodney's back.

'Slut' was carved into the top of his back. Not only carved but…entire strips of skin had been removed to make each letter. Then he saw the initials just under it. 'E.E.' and he wanted to hunt down this Domme and butcher her and bathe in her blood. But something told John that someone already did that. If this had been her idea of Scarification and marking then she was a sick, disturbed woman.

He led Rodney to the cross and took the wrist and ankle restraints from Lorne. Who was standing there with a sick a look on his face. He gently cuffed Rodney to the cross then went to stand in front of him.

"McKay do you understand what you're being punished for?" John asked as he pulled of his shirt and put it on the table.

"Yes. I put myself and Colonel Sumners team in danger. I almost got us all killed." John nodded his head in approval.

"You have the right to an advocate during this punishment. Is there someone you would like to give that responsibility to?"

"You Sir. I trust you to do all of my handling. Now and in the future too." John's eyes softened at the man.

"Okay. Here open." He spoke as he held the bite guard up to McKay's mouth.

"This will not be pleasurable. This is a punishment. And I punish hard. But I will not break the skin and draw blood since it was not requested as a part of your punishment, though I can for both pleasure and punishment. If this was a private punishment I would make you count the strikes, however as it is not, that won't be necessary. I will be concentrating on your back, ass, and thighs. If this was a private punishment I would map out each strike, however today I will not do such. We will take this in sets of ten. After each ten I will check your health. Do you understand?"

_Take this sinking boat and point it home, we've still got time._

The first ten were harsh, harder than Rodney would have expected. He groaned low and deep on the tenth. Then he felt hands gentle hands on him, soothing his back, ass, thighs. They were tender and seemed to know his body.

The next ten started and hurt much more than the first set. He bowed his head and felt something switch on in him. Emotions he hadn't felt in years. Safe. He was safe. And as crazy as it seemed he was comfortable in his punishment. The last of the ten made him cry out, but he controlled his body enough not to thrash or buck, knowing all too well the injuries that come with doing that.

Then John was standing in front of him checking his pulse and pupils. He felt a hand on the side of his face and he looked up in to soft eyes. Discipline Room or not, this was entirely private, this thing that was happening between them.

_Raise your hopeful voice you have a choice. You'll make it now_.

Then John was administering the last set, and Rodney felt tears slide down his face as he gave into his most basic instincts_. Relax. Let this Dom take care of me._ He felt his muscles relax and his body go slack, then he was there.

_Moods that take me and erase me and I'm painted black._

Yes it was a punishment and not for pleasure, but there was a deep catharsis in punishment that sent Subs tumbling into Subspace head over heels, yet at the same time a strong catharsis could only be reached once someone let go, submitted, surrendered. Rodney hadn't felt his Subspace in so long. Since before Tyler rescued him. He had wondered if he would ever feel it again.

_You've made it now. Falling slowly sing your melody. I'll sing it loud_

He felt John slide up in front of him and felt a hand sliding through his hair and over his tear stained face. The bite guard was removed. If anyone was surprised by what John did next Rodney couldn't tell as everyone was silent. He however was far from surprised by the lips on his own. A sweet, innocent, chaste kiss that said far too much.

Then it was over and he was being released and wrapped up in a robe. He was surrounded in John's arms, and he could barely think enough to care that they were surrounded by a crowd of their coworkers.

He felt himself being lowered to the ground and being cradled in strong arms. He rested his head on a strong shoulder and sighed. It had been too long, and Rodney had been too scared to ever act on his instincts and desires when it had come to Sheppard. All the bickering and fighting had been his way of coping with the aching desire he always felt near Sheppard. It seems like fate had taken that choice from him, scared or not.

He barely heard Elizabeth making people leave, and he barely heard the clicking of the door being shut. In this man's arms everything made sense. This was where he belonged. This was where his life had led him. He was scarred, broken, and damaged, but in this man's eyes he was beautiful. He was perfect. He had come home.

He felt lips on his and before he had time to process it, he had a hot slick tongue warring with his own. He felt a hand wrap around the back of his neck in imitation of a collar. He was home. How had he fought it off so long? There was something almost tangible linking them together. And if McKay were to believe in mysticism he would have believed it was a soul bond. But he was a man of science. But even Rodney's science was being pushed aside to make way for something deep, strong, and ancient.

_Take this sinking boat and point it home. We've still got time._

_**AN: Here you all go. Um…what can I say about this chapter? I have been where Rodney has been. My…I guess Domme you could call her, broke my heart and I was deeply suicidal. It took the care and attention of another Dom to heal me. He pulled me back from the brink. He gave me a reason to live. If not for myself then for him. He trained me and healed my broken soul. He not only healed me but gave me a self confidence in myself that is unshakeable. And with that self confidence came strength in myself, and love for myself. I have felt that powerful catharsis that comes with trusting a good Top with your care, even if it is a punishment. I chose to not be collared because I was still in love with her and he already had a Sub that was deeply in love with him. But I know where I belong. And I am comfortable and safe in that knowledge. Rodney's healing has only just begun though. There will be hard times for him, but with John there he will make it through it all. So it seems like I've blended a few ideas from a few stories and have made them my own, not just ones from Keira and Xanthe. So yes there is formal training in this story. I hope you all enjoyed and stay tuned for more.**_

_**Love all xoxox**_

_**Kat**_


	3. Chapter 2: Safe And Sound

_**AN: I apologize that it has taken me a few days to get this…rather small chapter written. I didn't quite know where to take the story after the punishment and I rewrote this chapter a few times before I found one I liked enough to keep. I originally wrote it as two weeks later, skipping all of the stuff in between. But it just didn't feel right. I do rather like aspects from that version of chapter two and will incorporate them eventually. EnJoY!**_

**Free Me, Free My Soul: Chapter Two: Safe And Sound**

_I remember tears streaming down your face_

After the punishment they went to the infirmary to have Carson check him over. It had been a clean punishment, and John was happy with his handiwork. He felt slightly guilty at kissing Rodney after it, when the Sub was so vulnerable. But then again Rodney had happily responded. And those kisses had said an entire novel of Rodney's feelings for him. John expected that Rodney had been head over heels crazy about him since…well ever.

He gazed at the submissive and felt a kind of pride that he hadn't felt since…since before he'd been put on ice at McMurdo. He had done right by a Sub. And in this Sub's eyes he was-safe. Safe. And in John's arms he was safe and sound.

He smiled as he gazed down at Rodney. He ran his hand through Rodney's messy, too long, sweat matted hair. Rodney looked up at him and his eyes said a million things. 'I'm broken. I'm damaged goods. I'm lost. Please don't hurt me.' And John sighed. He bent his head until their foreheads touched. He wanted to give this damaged Sub everything he could. Carson looked from John to Rodney and back again before he left. He pulled a chair up to McKay's bed and simply held his hand. Carson wanted to keep him over night and do a complete medical in the morning. For now he was content to sit by the Sub's bed side all night.

_When all those shadows almost killed your light._

Rodney looked at John with sad, clouded eyes. John picked the hand up and kissed it softly. "Did she get what she deserved Rodney?"

"Meredith. Call me Meredith. And yes. Tyler…and a few other masters from his pleasure house took care her. They didn't waste time by charging her with anything. Why would they when their pleasure master, who is a court appointed judge, ordered the hit? Apparently I wasn't her first abused Sub and they were just looking for a reason to gut her. I apparently gave them that reason. They justified it by saying it was their responsibility for taking her out of this world since they were the ones that created her in a way."

_But all that's dead and gone and passed tonight._

John sat up. He looked at Rodney a little stupidly. "Meredith Elias. That was you? That…cunt…was your Domme? You are the Sub I avenged? Tyler as in Matthew Tyler Phillippe, trained De Sade Master?" Rodney looked up at him with wide shocked eyes.

"Shit. You're one of François Phillippe's trained masters. Fuck. Your uncensored file didn't say that. It just said you were a De Sade master. I guess you know the answer to your own question then."

John blinked slowly. François had made the executive decision to have her taken out of the world because of her insanely unstable dynamic. François had excused her half way into her first session at De Sade because she was so unsafe. He had kept close tabs on her over the years and had taken care of the various Subs she abused when she was done with them. Normally that meant that they had inadvertently ended up hospitalized, and François would have them placed under protective custody, their collar lying on the bed in their place.

Rodney had been an unfortunate mistake as François had missed his narrow window to get the Sub safely out of the hospital. John guessed that was where Matt had come in. It had been a brilliant plan to place his only son, a scientist no less, in the same department at the same company that Rodney was at the time working at. Once Rodney got to know him and trust him, he reached out for help, just as he was supposed to. After Rodney was removed to a safe location François' trained masters were called in to 'handle the cunt that threatens the wellbeing of Submissives everywhere'. It had been his and the others extreme pleasure to do exactly that.

As he was putting this all together in his head, Rodney was as well. He smiled at John and gave a low chuckle. "I guess people in high places were looking out for me. No wonder François Phillippe invited me to train at De Sade. I so wanted to too. But work got crazy then I got transferred to the SGC then to Antarctica, then to here. I should have taken the offer. But work came first. I guess once he realized that he made sure I was transferred somewhere worthy of my big brain." McKay rolled his head sleepily to one side.

_Don't you dare look out your window, darling, everything's on fire._

"Tell me you gutted her Sheppard. Tell me her blood sprayed the walls the way mine did when she scarred me."

"Yes. We butchered her. We had orders to make her suffer long and hard. At the end I stuck my knife into her belly and gutted her like a fish. Then we gathered up her remains and dumped them at the police station with a note attached to her shirt saying 'I abused Submissives for a living. Guess I abused one too many.'"

McKay grinned at this. "Good. She deserved it." John nodded his head and stroked his hand down the side of Rodney's face. "Out of all of her Subs you were the one least damaged. But like the note said, you were the one she shouldn't have ever picked up."

"How did she get away with it for so long?" Rodney questioned curiously.

"She had the entire night shift at the local ER bribed and blackmailed. When François found proof of it, he had them all brought up on charges."

Rodney laughed cynically. "I guess he saved the world a few Subs at a time then. Stay, John please. Don't leave me here alone."

_The war outside our door keeps raging on._

"Just close your eyes, Meredith. You'll be alright. No one can hurt you now. You're safe and sound with me."

Rodney nuzzled his cheek into John's hand and felt himself drift off to sleep. And just when we about to sleep he heard John mutter, "I'll never let you go."

_Come morning light, you and I'll be safe and sound._

_**AN: I decided to use keira's pleasure house in my story, but the characters are all new and all mine. The song is safe and sound by taylor swift. Hmm I should have a playlist generated by next chapter. if anyone is curious I imagine Matt aka Tyler to look like Ryan Phillippe. And his father to look like viggo mortensen. Aahaha im a sucker for hot men. **_


	4. generated playlist

_**AN: here is the generated playlist for this story. Its safe to say that ive thought this story out now. I want this story to be raw and edgy with its angsty, fluffy, sweet, loving, tender moments so more than a lot of this playlist is EDM, specificly krewella ,david guetta, adventure club, and knife party. Mostly krewella. So this might change. But im more than happy with it and will try to keep the chapters to this basic outline biggest thing about this story is that it has two main pairings. Sheppard/McKay and Lorn/OC. And both pairings have things to overcome and maybe not overcome. **_

Opening Theme: One Minuet Kewella

Main Theme One: Falling Slowly Chester See

Main Theme Two: I'm Your Angel - and Celine Dion

Closing Theme: Rise and Fall Adventure Club and Krewella

One Minute Krewella

Falling Slowly Chester See

Safe and Sound

Feel Me Krewella

Fairytale Jessica Sanchez (Evan muses)

Come and Get It Krewella (from e.e. to j.s.)

Can't Control Myself Krewella

My All Jessica Sanchez

Play Hard (Ty's Theme)

Tonight Jessica Sanchez and Ne Yo

Crave You Adventure Club

Fire Hive Knife Party and Krewella

Just One Last Time David Guetta and Trapped Rai

Try Nelly Furtado

Heart Jessica Sanchez

Yes To Love Sefano

Rise and Fall Adventure Club and Krewella


End file.
